I'm too lazy to do a full writeup right now, but I took some screengrabs to demonstrate how to load MSU-1 games in higan without any need for a manifest, as well as how to load a .msu1 pack in Snes9x, so I figured they were worth sharing here as well. Sometimes, a picture is worth 1000 words. The main thing to notice is the filenames. Snes9x/SD2SNES files must match the ROM name, higan always uses msu1.rom and track-#.pcm regardless (unless you have a manifest which explicitly overrides that), and also higan requires that the folder name end with ".sfc".

higan:

Snes9x/SD2SNES:

Snes9x w/.msu1 pack*:

*note that a .msu1 pack also includes the patch file, so the ROM should be the original, unmodified game. In the other cases, you should apply the patch to the ROM file manually.